A hotspot of diversity: novel Shewanella species isolated from Baltic Sea sediments delineate a sympatric species complex

Two bacterial strains, SP1S1-4^T and SP2S1-2^T, were isolated from sediment samples collected in the Stockholm archipelago in November 2021. Following whole-genome sequencing, these strains were identified as tentatively belonging to two novel <i>Shewanella</i> genospecies, based on digital DNA-DNA hybridization, as implemented in the Type Strain Genome Server. <i>Shewanella septentrionalis</i>, <i>Shewanella baltica</i> and <i>Shewanella hafniensis</i> were, in this order and within a narrow genomic relatedness range, their closest genotypic relatives. Additional sampling and sequencing efforts led to the retrieval of distinct isolates that were monophyletic with SP1S1-4^T and SP2S1-2^T, respectively, based on phylogenomic analysis of whole-genome sequences. Comparative analyses of genome sequence data, which included blast-based average nucleotide identity, core genome-based and core proteome-based phylogenomics, in addition to MALDI-TOF MS-based protein profiling, confirmed the distinctness of the putative novel genospecies with respect to their closest genotypic relatives. A comprehensive phenotypic characterisation of SP1S1-4^T and SP2S1-2^T revealed only minor differences with respect to the type strains of <i>S. septentrionalis</i>, <i>S. baltica</i> and <i>S. hafniensis</i>. Based on the collective phylogenomic, proteomic, and phenotypic evidence presented here, we describe two novel genospecies within the genus <i>Shewanella</i>, for which the names <i>Shewanella scandinavica</i> sp. nov. and <i>Shewanella vaxholmensis</i> sp. nov. are proposed. The type strains are, respectively, SP2S1-2^T (=CCUG 76457^T=CECT 30688^T), with a draft genome sequence of 5 041 805 bp and a G+C content of 46.3 mol%, and SP1S1-4^T (=CCUG 76453^T=CECT 30684^T), with a draft genome sequence of 4 920147 bp and a G+C content of 46.0 mol%. Our findings suggest the existence of a species complex formed by the species <i>S. baltica</i>, <i>S. septentrionalis</i>, <i>S. scandinavica</i> sp. nov., and <i>S. vaxholmensis</i> sp. nov., with <i>S. hafniensis</i> falling in the periphery, where distinct genomic species clusters could be identified. However, this does not exclude the possibility of a continuum of genomic diversity within this sedimental ecosystem, as discussed herein with additional sequenced isolates.